With the development of next generation sequencing (NGS) technology, the variation of sequences represented as SNP between cultivars becomes available at genome level. The major domestic cultivars with high yield have been developed by breeding of indica and japonica, it is important to localize the region of origin according to the genotype for further characterization of unique features of cultivars. For the localization of SNP at genome level, the paired end sequences of 6 major domestic rice cultivars, Ilmi, Ilpoom, Sulgaeng, Bakjinju, Hwayoung and Woonkwang were compared against Japonica and Indica Rice Genomes as reference genomes. The genomic DNAs were prepared from callus tissues and paired-end of the fragments were sequenced with NGS Sequencer, Illumina HISeq. About 50x coverage of paired-end sequences were trimmed according to the quality of the sequences, and errors were corrected with statistical analysis of kmers of 15. The trim-corrected sequences were mapped and variants were analyzed against reference genomes. The overall change rate of Ilmi against Nipponbare IRGSP 1.0 and Indica BGI 93-11 reference genomes were 0.92 base/1kb (1/1,079 base) and 8.09 base/1kb (1 base/123 bases), respectively. Among 6 cultivars, overall rate of Bakjinju showed the lowest overall change rate of 0,53 base/1kb, and Hwayoung showed highest frequency of 0.92 base/1kb. Compared to high level in the range of change rate of 7.0-9.3 base/1kb against indica, domestic cultivars showed lower range of change rate 0.2-3.3 base/1kb with unique local high peak against japonica genome depend on the chromosomes. Compared to assembly of genome sequences, the variation of nucleotides compared to reference sequences is much faster and simple to characterize the genotype. The types of variation and the effect on functional categories will be presented.